you shouldn't have any trouble getting it on board there's nothing illegal about it... I've carried mine through airports several times and am actually yet to even be stopped so you shouldn't have any trouble getting it on board.
I agree with the other folks saying you should definitely talk to the captain about it if you plan on launching from the ship itself, and respect his orders regardless of what they are. I'd definitely offer to share the videos with him! I'd also take the opportunity to ask him if he thinks the ship is doing much in the 2.4 or 5.8Ghz frequency ranges (interference), if he doesn't know he can direct you to someone that does but those are consumer bands the ship probably won't directly interfere on the same frequencies except for their local wifi, but I'd still stay away from the antennas in general.
I'm a risk taker... when you fly is up to how much risk you're willing to take... how awesome would ship under sail footage be?! I HIGHLY recommend you get good at catching! imo catching a Phantom can be safer than ground landing if you're careful and practiced and it's the only way you're getting the phantom back if you fly while the ship is under sail. imo there is a perfect catch at the beginning of
this video, approach from above, set your height, use one hand to control lateral movement and reach up and out to catch it. I'd recommend having a neck strap if you don't already.
I would ask the captain what speed he typically cruises at someone here mentioned 21 to 24 knots (24 knots = almost 28mph), that's below the ~33 mph max speed in GPS mode people are getting. supposedly ATTI has a higher max speed but remember if you have a headwind that would affect your ground speed.
so let's put the "under sail" part to rest and talk about launching from port or anchor, and how it would relate to GPS/home lock. I've gotten perfectly good gps/home lock from wooden surfaces with metal underneath, which the back decks of the ship should be. As long as there's a couple inches of wood between the metal you should be fine... just watch the indicator lights you're familiar with those right? If I fire up the phantom on a metal outdoor table, car, or I even accidentally put it on a metal grate that was barely covered by grass once the rear lights will never do that rapid green flash, my P2 just blinks constant yellow but as soon as I move it away from the metal the lights flash green and you're gtg.
These sound like short distance flights, as long as your batteries are good you hopefully won't need failsafe/RTH which wouldn't work under sail anyway.
lastly, imo every pilot should be aware and accept the risk if you're going to fly over water. ANYTHING can happen from equipment failure to a bird strike to lord knows what, and you should mentally prepare yourself for a total loss before it actually happens. If you're not willing to lose your toy, then don't fly over water. risk vs reward
good luck! be sure to post your videos!